[gmx-users] MW4?

[Anton Feenstra]

Outi Maija Salo wrote:
> 
> Hi!
> 
> I am trying to do an MD run for my protein using opls force field and
> tip4p water.
> 
> When I did genbox the program said that:
> 
> Output configuration contains 128066 atoms in 31018 residues
> WARNING: masses will be determined based on residue and atom names,
>          this can deviate from the real mass of the atom type
> Opening library file /appl2/gromacs-3.1.4/share/top/atommass.dat
> Mass of atom SOL MW4 set to 12.011
> Volume                 :     991.746 (nm^3)
> Density                :     1606.13 (g/l)
> Number of SOL molecules:  30678
> 
> Should not this SOL MW4 be a dummy atom and thus set to 0.0 ???
> There is no such SOL  MW4 in atommass.dat. Should I add it?

atommass.dat is only used by some analysis tools, that do not
know about atom types and their corresponding masses, but instead
try to derive the mass from the atom *name*. But, you are right,
in this case you don't want to count any mass from the MW4.


-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Vrije Universiteit Amsterdam |
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